Ceballos, I. C. | bioRxiv Science

bioRxiv2025

Diurnal plant and Rhizophagus irregularis transcriptional patterns are linked to shifts in cassava tissue partitioning in the field

O_LICassava is a globally-important crop whose yields can radically increase with arbuscular mycorrhizal fungi (AMF) inoculation. However, extensive background noise in field environments makes it very challenging to understand how the cassava-AMF symbiosis confers benefits, which is especially important for future applications of AMF treatments. C_LIO_LIIn two field experiments, we combined transcriptomics and allometric analyses to investigate functional variation in cassava-AMF interactions using sterile, single isolates of Rhizophagus irregularis. We developed a novel Index of Symbiotic Transcriptional Activity (ISTA) and accounted for sampling times to reduce transcriptomic noise and improve links to biomass traits. C_LIO_LIISTA significantly correlated with cassava shoot biomass in an isolate-dependent manner, and allometric analyses revealed that R. irregularis isolates can either reinforce or uncouple cassava shoot-root relationships to maximize root yields. Differential expression and co-expression network analyses uncovered isolate-specific plant and fungal gene module responses. Including ISTA and sampling time as random effects enhanced detection of gene candidates, including down-regulated genes linked to higher yield. C_LIO_LIOur study uses novel and translatable transcriptomic tools to readily dissect variably field data, allowing new links to be found between AMF symbiotic functions and cassava yields. C_LI

molecular biology↗

bioRxiv2019

Using variation in arbuscular mycorrhizal fungi to drive the productivity of the food security crop cassava

The unprecedented challenge to feed the rapidly growing human population can only be achieved with major changes in how we combine technology with agronomy1. Despite their potential few beneficial microbes have truly been demonstrated to significantly increase productivity of globally important crops in real farming conditions2,3. The way microbes are employed has largely ignored the successes of crop breeding where naturally occurring intraspecific variation of plants has been used to increase yields. Doing this with microbes requires establishing a link between variation in the microbes and quantitative traits of crop growth along with a clear demonstration that intraspecific microbial variation can potentially lead to large differences in crop productivity in real farming conditions. Arbuscular mycorrhizal fungi (AMF), form symbioses with globally important crops and show great potential to improve crop yields2. Here we demonstrate the first link between patterns of genome-wide intraspecific AMF variation and productivity of the globally important food crop cassava. Cassava, one of the most important food security crops, feeds approximately 800 million people daily4. In subsequent field trials, inoculation with genetically different isolates of the AMF Rhizophagus irregularis altered cassava root productivity by up to 1.46-fold in conventional cultivation in Colombia. In independent field trials in Colombia, Kenya and Tanzania, clonal sibling progeny of homokaryon and dikaryon parental AMF enormously altered cassava root productivity by up to 3 kg per plant and up to a 3.69-fold productivity difference. Siblings were clonal and, thus, qualitatively genetically identical. Heterokaryon siblings can vary quantitatively but monokaryon siblings are identical. Very large among-AMF sibling effects were observed at each location although which sibling AMF was most effective depended strongly on location and cassava variety. We demonstrate the enormous potential of genetic, and possibly epigenetic variation, in AMF to greatly alter productivity of a globally important crop that should not be ignored. A microbial improvement program to accelerate crop yield increases over that possible by plant breeding or GMO technology alone is feasible. However, such a paradigm shift can only be realised if researchers address how plant genetics and local environments affect mycorrhizal responsiveness of crops to predict which fungal variant will be effective in a given location.

microbiology↗